Workflow

MT lineage tracing pipeline

Outdir is /data/Mito_Trace/output Preifx is cd34norm/MTblacklist

Click the nodes to obtain details about each step.

Multiplex

Nuclear ATAC

QC

Other

Variants

lineage

enrichment

mtpreproc

Other

filter

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
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## Global params
outdir: "/data/Mito_Trace/output" # Global output directory
config: "parameters/pipeline/pipeline.yaml"
#params: "parameters/pipeline/params.csv"

## Experiment params
prefix: "cd34norm/MTblacklist"
samples_meta: "parameters/pipeline/cosmo_server/jan21_2021.csv"
genome: "MTBlacklist"
fastq_dir: "/data2/isshamie/mito_lineage/data/raw/jan21_2021_Croker/" #igm-storage2.ucsd.edu/210114_A00953_0213_AHVM25DSXY"
mtscATAC_OUTDIR: "/home/isaac/lewis/mito_lineage/output/mtscATAC/data/jan21_2021/MTblacklist"
#results: "/data/isshamie/mito_lineage/output/pipeline/cd34norm/MTblacklist" # Output directory
N_DONORS: 4

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